Abstract B013: T cell clonotype expansion is common in advanced renal cell carcinoma but is not associated with altered response to PD-1 blockade
Authors: Miya B. Hugaboom, Neil Ruthen, Opeyemi Jegede, Nicholas R. Schindler, Lena Wirth, Sasha Kyrysyuk, David F. McDermott, Elizabeth R. Plimack, Jeffrey A. Sosman, Naomi B. Haas, Michael E. Hurwitz, Hans J. Hammers, Sabina Signoretti, Michael B. Atkins, Catherine J. Wu, David A. Braun, Kelly Street
Journal: Cancer Research (2023)

Abstract The diversity of T cell receptors (TCRs) becomes increasingly restricted with advancing stage in renal cell carcinoma (RCC), with individual T cell clones becoming dramatically expanded. Further, prior studies have suggested that TCR clonality (i.e. less diversity) could be associated with improved clinical response to anti-PD-1 treatment. To further interrogate the TCR landscape of advanced RCC and its relation to both T cell phenotype and clinical outcomes, single-cell TCR sequencing (scTCR-seq) was performed in parallel with single-cell RNA sequencing (scRNA-seq) for eligible patients with clear cell or non-clear cell metastatic RCC both pre- (baseline) or post- (progression) treatment with front-line nivolumab monotherapy as part of the HCRN GU16-260 trial (NCT03117309). Clonotype assignments and diversity metrics for 19 tumor samples were determined using VDJdive (R/Bioconductor). Overall, the top 10 clonotypes accounted for 12.3% of all T cells (range by sample: 4.2-34.6%). Of note, 5 of 16 (31%) samples with at least 100 T cells displayed substantial clonotype expansion, with the top 10 clonotypes accounting for at least 20% of tumor-infiltrating T cells. Average TCR diversity (normalized Shannon entropy) was 0.55 (range: 0.38-0.91) for all 19 samples. There were no significant differences in T cell diversity both between baseline (n=10) and post-treatment (n=9) samples (p= 0.66) or between clear cell (n=14) and non-clear cell (n=5) histologies (p= 0.75). To assess the relationship between T cell specificity and phenotypic state, we investigated the distribution of the most expanded clonotypes along a trajectory of T cells. Previous trajectory analysis of T cell populations revealed a bifurcating structure with naïve T cells at the root and lineages terminating in either terminally exhausted CD8+ T cells or SLAMF7+ CD8+ T cells (Braun, ASCO GU, 2023). Of the top 20 most expanded clonotypes across all T cells, 95% were distributed almost exclusively in the terminally exhausted lineage. The TCR diversity decreased along each lineage, from naïve T cell cluster at the root (TCR diversity = 0.61) to either the terminally exhausted CD8+ T cell cluster (0.42) or the SLAMF7+ CD8+ T cell cluster (0.56). There were no significant differences in TCR diversity between patients with progressive disease (n=6) versus complete/partial response (n= 6), (p= 0.96). Similarly, there was no association between TCR diversity and either progression-free (p= 0.41) or overall (p=0.39) survival. Altogether, these data reaffirm the presence of clonal expansion in advanced RCC, with the degree varying by sample. The localization of most expanded clonotypes to a single T cell lineage suggests a low degree of phenotypic plasticity. Enrichment of these clonotypes along an exhausted lineage is consistent with prior findings of lower TCR diversity in terminally exhausted CD8+ T cells. Future directions will focus on inferring the tumor specificity of infiltrating T cells along the diverging lineages. Citation Format: Miya B. Hugaboom, Neil Ruthen, Opeyemi Jegede, Nicholas R. Schindler, Lena Wirth, Sasha Kyrysyuk, David F. McDermott, Elizabeth R. Plimack, Jeffrey A. Sosman, Naomi B. Haas, Michael E. Hurwitz, Hans J. Hammers, Sabina Signoretti, Michael B. Atkins, Catherine J. Wu, David A. Braun, Kelly Street. T cell clonotype expansion is common in advanced renal cell carcinoma but is not associated with altered response to PD-1 blockade [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B013.